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Detailed information for vg0432712400:

Variant ID: vg0432712400 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32712400
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGACCGGACGAGTAGCACTGTCTCATCCGTGTCGTTTGAGAAGCACTCACTTAGTTGTTTTTAGAAAAGAGCTCAAATAAAATAAATTGCAAAAACAACA[G/A]
CCTTTCTTTGAAGCCTGCATTAAACACTTATTTCCTATGGCTTGCTGAGTACTCCCGTACTCACCCTTGCTCTATATAAATAACCCCCCCGCAGTTGCTG

Reverse complement sequence

CAGCAACTGCGGGGGGGTTATTTATATAGAGCAAGGGTGAGTACGGGAGTACTCAGCAAGCCATAGGAAATAAGTGTTTAATGCAGGCTTCAAAGAAAGG[C/T]
TGTTGTTTTTGCAATTTATTTTATTTGAGCTCTTTTCTAAAAACAACTAAGTGAGTGCTTCTCAAACGACACGGATGAGACAGTGCTACTCGTCCGGTCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.40%	7.20%	12.76%	33.64%	NA
All Indica	2759	41.50%	1.00%	17.91%	39.65%	NA
All Japonica	1512	56.30%	18.40%	3.11%	22.16%	NA
Aus	269	49.40%	4.80%	11.52%	34.20%	NA
Indica I	595	31.80%	2.90%	36.47%	28.91%	NA
Indica II	465	32.50%	0.40%	8.60%	58.49%	NA
Indica III	913	56.40%	0.00%	10.08%	33.52%	NA
Indica Intermediate	786	36.80%	1.00%	18.45%	43.77%	NA
Temperate Japonica	767	77.30%	8.20%	1.69%	12.78%	NA
Tropical Japonica	504	36.70%	37.50%	4.96%	20.83%	NA
Japonica Intermediate	241	30.70%	10.80%	3.73%	54.77%	NA
VI/Aromatic	96	30.20%	15.60%	10.42%	43.75%	NA
Intermediate	90	38.90%	7.80%	23.33%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0432712400	G -> DEL	N	N	silent_mutation	Average:6.562; most accessible tissue: Callus, score: 14.602	N	N	N	N
vg0432712400	G -> A	LOC_Os04g55020.1	upstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:6.562; most accessible tissue: Callus, score: 14.602	N	N	N	N
vg0432712400	G -> A	LOC_Os04g55000-LOC_Os04g55020	intergenic_region ; MODIFIER	silent_mutation	Average:6.562; most accessible tissue: Callus, score: 14.602	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432712400	3.73E-06	NA	mr1988	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251